I like the idea of Shanthi being the C-in-C of Starfleet (which, according to Memory Beta is a separate position from "Commander, Starfleet," and "Chief of Staff for the Federation Starfleet," also an idea which I like), and, at least, in some of the Myriad Universes stories I'm rereading, that is how she is treated.
As for characters to be killed, I've said this before: Vale. Not really for story purposes, but just because I don't like her.